The long-term goals of our laboratory are to understand how noncoding RNAs function, how cells recognize and degrade defective and unneeded RNAs, and how failure to degrade these RNAs affects cell function and contributes to human disease. A major focus is an abundant class of ribonucleoproteins (RNPs), known as Ro60 RNPs, which are widespread in animal cells and also present in many bacteria. Ro60 RNPs were discovered because the major protein, the ring-shaped Ro 60 kDa autoantigen, is a clinically important target of autoantibodies in patients with systemic lupus erythematosus and Sjogren's syndrome. In all organisms examined, Ro60 binds noncoding RNAs called Y RNAs. By studying Ro60 RNPs in the bacterium Deinococcus radiodurans, and extending our findings to mammalian cells, we uncovered a novel role for ncRNA, that of tethering a protein cofactor to an effector protein to alter its function. Specifically, we discovered that a bacterial Ro60 was tethered by Y RNA to a ring-shaped exoribonuclease, forming a new double-ringed RNA degradation machine. We also showed that mammalian Y RNAs also tether Ro60 to effector proteins. Our laboratory continues to define roles for Ro60 ribonucleoproteins in mammalian cells and bacteria and to elucidate the ways in which RNA surveillance pathways contribute to cell physiology. To identify Ro60 targets in mammalian cells, we combined high-throughput sequencing of RNA after in vivo crosslinking and immunoprecipitation (HITS-CLIP) with whole transcriptome analyses (RNA-Seq). The mechanisms by which Ro60 and Y RNAs contribute to the metabolism of the identified RNA targets is under investigation. In bacteria, our recent experiments have been carried out in the human pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), a genetically tractable enteric bacterium closely related to Escherichia coli. Our studies revealed a new subfamily of bacterial Y RNAs in which the effector-binding domain is predicted to fold to resemble tRNA. Structural studies, carried out with Yong Xiong (Yale University), confirmed that this domain is a close tRNA mimic. We also discovered that, in S. Typhimurium and many other bacteria, Ro60 and Y RNAs are encoded within a highly regulated RNA repair operon that also includes the RtcB RNA ligase. We are dissecting both the ways in which this operon is regulated and the roles of Ro60 and Y RNAs in S. Typhimurium. Lastly, we collaborated with Martin Kriegel (Yale University) to test the hypothesis that commensal Ro60-containing bacteria could trigger and sustain production of anti-Ro60 antibodies in genetically susceptible patients. Thus, our discovery and characterization of bacterial Ro60 RNPs has contributed to a novel hypothesis for how autoimmune diseases such as systemic lupus erythematosus arise and may lead to novel therapeutic approaches.